cellular reprogramming

细胞重编程
  • 文章类型: Journal Article
    背景:子宫内膜癌是主要的妇科肿瘤之一,在过去的几十年中,发病率和死亡率不断上升。新兴的临床前和临床数据表明其与肥胖和血脂异常密切相关。代谢重编程被认为是癌症的标志,以满足生存和生长对营养和能量的广泛需求。特别是,脂质代谢重编程引起了研究人员对癌症领域的兴趣,包括肿瘤发生,侵入性,转移,治疗抗性和免疫调节,等。但是脂质代谢重编程在子宫内膜癌中的作用尚未完全了解。本文就脂质代谢重编程诱导子宫内膜癌的发生发展作一综述。包括脂质代谢途径的生物学功能异常和脂质代谢途径的转录调控改变。此外,我们提出了靶向脂质代谢途径的新治疗策略,并集中于其敏化免疫疗法和激素疗法的潜力,进一步优化晚期/转移性子宫内膜癌患者的现有治疗方式。此外,我们预计,靶向脂质代谢加激素治疗可能阻断子宫内膜恶变,丰富子宫内膜癌的预防方法。
    结论:脂质代谢重编程在子宫内膜癌的肿瘤发生和进展中起重要作用。单独或联合免疫疗法/激素治疗靶向脂质代谢途径的核心酶和转录因子有望减轻肿瘤负担,并为晚期/转移性子宫内膜癌患者提供有希望的治疗机会。
    BACKGROUND: Endometrial cancer is one of the major gynecological cancers, with increasing incidence and mortality in the past decades. Emerging preclinical and clinical data have indicated its close association with obesity and dyslipidemia. Metabolism reprogramming has been considered as the hallmark of cancer, to satisfy the extensive need of nutrients and energy for survival and growth. Particularly, lipid metabolism reprogramming has aroused the researchers\' interest in the field of cancer, including tumorigenesis, invasiveness, metastasis, therapeutic resistance and immunity modulation, etc. But the roles of lipid metabolism reprogramming in endometrial cancer have not been fully understood. This review has summarized how lipid metabolism reprogramming induces oncogenesis and progression of endometrial cancer, including the biological functions of aberrant lipid metabolism pathway and altered transcription regulation of lipid metabolism pathway. Besides, we proposed novel therapeutic strategies of targeting lipid metabolism pathway and concentrated on its potential of sensitizing immunotherapy and hormonal therapy, to further optimize the existing treatment modalities of patients with advanced/metastatic endometrial cancer. Moreover, we expect that targeting lipid metabolism plus hormone therapy may block the endometrial malignant transformation and enrich the preventative approaches of endometrial cancer.
    CONCLUSIONS: Lipid metabolism reprogramming plays an important role in tumor initiation and cancer progression of endometrial cancer. Targeting the core enzymes and transcriptional factors of lipid metabolism pathway alone or in combination with immunotherapy/hormone treatment is expected to decrease the tumor burden and provide promising treatment opportunity for patients with advanced/metastatic endometrial cancer.
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  • 文章类型: Journal Article
    背景:iPSC重编程技术在临床治疗领域具有重要的前景,疾病建模,药物发现,和其他各种应用。然而,这项技术的广泛利用遇到了效率低下的障碍,延长程序,和模糊的生物过程。因此,为了改进这项技术,深入研究iPSC重编程的底层机制具有重要意义。BET蛋白BRD4在重编程的后期起关键作用;然而,其早期的确切功能尚不清楚。
    结果:我们的研究旨在探讨BRD4在iPSC重编程早期阶段的作用。我们的研究表明,BRD4的早期抑制实质上增强iPSC重编程,而中后期的实施阻碍了这一进程。在重新编程的过程中,核糖体DNA表达最初增加,然后减少,然后逐渐恢复。早期抑制BRD4改善了早期和中晚期rDNA表达的下降和恢复,分别。此外,我们发现了BRD4在整个重编程过程中对rDNA转录的调控机制。具体来说,BRD4与UBF相互作用并共定位到rDNA启动子和增强子区。最终,BRD4通过促进周围染色质中组蛋白H3赖氨酸27乙酰化的富集来促进rDNA转录。此外,我们还发现,BRD4的早期抑制促进细胞从体细胞状态转变并激活多能基因.
    结论:结论:我们的结果表明,早期抑制BRD4促进rDNA的顺序动态表达,提高了iPSC重编程效率。
    BACKGROUND: iPSC reprogramming technology exhibits significant promise in the realms of clinical therapeutics, disease modeling, pharmaceutical drug discovery, and various other applications. However, the extensive utilization of this technology has encountered impediments in the form of inefficiency, prolonged procedures, and ambiguous biological processes. Consequently, in order to improve this technology, it is of great significance to delve into the underlying mechanisms involved in iPSC reprogramming. The BET protein BRD4 plays a crucial role in the late stage of reprogramming; however, its precise function in the early stage remains unclear.
    RESULTS: Our study aims to investigate BRD4\'s role in the early stages of iPSC reprogramming. Our investigation reveals that early inhibition of BRD4 substantially enhances iPSC reprogramming, whereas its implementation during the middle-late stage impedes the process. During the reprogramming, ribosome DNA expression initially increases before decreasing and then gradually recovers. Early inhibition of BRD4 improved the decline and restoration of rDNA expression in the early and middle-late stages, respectively. Additionally, we uncovered the mechanism of BRD4\'s regulation of rDNA transcription throughout reprogramming. Specifically, BRD4 interacts with UBF and co-localizes to both the rDNA promoter and enhancer regions. Ultimately, BRD4 facilitates rDNA transcription by promoting the enrichment of histone H3 lysine 27 acetylation in the surrounding chromatin. Moreover, we also discovered that early inhibition of BRD4 facilitates cells\' transition out of the somatic cell state and activate pluripotent genes.
    CONCLUSIONS: In conclusion, our results demonstrate that early inhibition of BRD4 promotes sequential dynamic expression of rDNA, which improves iPSC reprogramming efficiency.
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  • 文章类型: Journal Article
    代谢重编程为肿瘤提供了能量来源和生物燃料,以支持其在恶性微环境中的生存。对肿瘤微环境(TME)的内在致癌机制的广泛研究已经确定,癌症相关成纤维细胞(CAFs)和代谢重编程通过许多生物学活性调节肿瘤进展。包括肿瘤免疫抑制,慢性炎症,生态位重塑。具体来说,通过共同支持慢性炎症的CAFs和多种免疫细胞促进免疫抑制性TME形成,释放介质,从而诱导转移前生态位的形成,并最终推动肿瘤增殖和转移的恶性循环。本文综述了肿瘤适应性TME动态演化的CAFs和代谢调控过程,特别关注CAFs促进免疫抑制微环境形成和支持转移的机制。现有的发现证实了TME的多个组成部分协同作用以加速肿瘤事件的进展。在推进与CAF相关的研究的背景下,进一步讨论了基于CAF的靶向治疗在临床环境中的潜在应用和挑战。
    Metabolic reprogramming provides tumors with an energy source and biofuel to support their survival in the malignant microenvironment. Extensive research into the intrinsic oncogenic mechanisms of the tumor microenvironment (TME) has established that cancer-associated fibroblast (CAFs) and metabolic reprogramming regulates tumor progression through numerous biological activities, including tumor immunosuppression, chronic inflammation, and ecological niche remodeling. Specifically, immunosuppressive TME formation is promoted and mediators released via CAFs and multiple immune cells that collectively support chronic inflammation, thereby inducing pre-metastatic ecological niche formation, and ultimately driving a vicious cycle of tumor proliferation and metastasis. This review comprehensively explores the process of CAFs and metabolic regulation of the dynamic evolution of tumor-adapted TME, with particular focus on the mechanisms by which CAFs promote the formation of an immunosuppressive microenvironment and support metastasis. Existing findings confirm that multiple components of the TME act cooperatively to accelerate the progression of tumor events. The potential applications and challenges of targeted therapies based on CAFs in the clinical setting are further discussed in the context of advancing research related to CAFs.
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  • 文章类型: Journal Article
    三阴性乳腺癌(TNBC)因其高侵袭性而成为乳腺癌治疗中的棘手问题,转移和复发。尽管免疫疗法在TNBC中取得了重要进展,多种因素引起的免疫逃逸,尤其是代谢重编程,仍是TNBC免疫治疗的瓶颈。遗憾的是,导致免疫逃逸的机制仍然知之甚少。在代谢水平探索TNBC免疫逃逸的机制为后续靶向或免疫治疗提供了靶点和方向。在这次审查中,我们关注TNBC通过缺氧影响免疫细胞和间质细胞的机制,葡萄糖代谢,脂质代谢和氨基酸代谢,改变肿瘤代谢和肿瘤微环境。这将有助于为TNBC免疫治疗寻找新的靶点和策略。
    Triple-negative breast cancer (TNBC) has become a thorny problem in the treatment of breast cancer because of its high invasiveness, metastasis and recurrence. Although immunotherapy has made important progress in TNBC, immune escape caused by many factors, especially metabolic reprogramming, is still the bottleneck of TNBC immunotherapy. Regrettably, the mechanisms responsible for immune escape remain poorly understood. Exploring the mechanism of TNBC immune escape at the metabolic level provides a target and direction for follow-up targeting or immunotherapy. In this review, we focus on the mechanism that TNBC affects immune cells and interstitial cells through hypoxia, glucose metabolism, lipid metabolism and amino acid metabolism, and changes tumor metabolism and tumor microenvironment. This will help to find new targets and strategies for TNBC immunotherapy.
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  • 文章类型: Journal Article
    从成体细胞产生的诱导多能干细胞(iPSC)被诱导表达通过重编程技术使其具有多能性的基因。凭借其无限的增殖能力和多方面的分化潜力,并规避了胚胎干细胞(ESC)应用中遇到的伦理问题,iPSCs在细胞治疗领域有着广泛的应用,药物筛选,和疾病模型,并可能为未来再生医学治疗疾病开辟新的可能性。在这次审查中,我们从不同的重编程细胞技术开始获得iPSCs,包括生物技术,化学,和物理调制技术,展示各自的长处,和限制,以及最近的研究进展。其次,我们综述了基于iPSC重编程的再生疗法的最新研究进展.iPSCs目前被广泛用于研究毛囊缺损的各种临床疾病,心肌梗塞,神经系统疾病,肝脏疾病,和脊髓损伤。本文重点介绍了iPSCs的转化临床研究及其在医学领域的发展潜力。最后,我们总结了总体综述,并展望了iPSCs在细胞治疗以及组织再生工程领域的潜在前景和可能存在的问题。我们相信,正在推进的iPSC研究将有助于推动期待已久的细胞治疗突破。
    Induced pluripotent stem cells (iPSCs) that are generated from adult somatic cells are induced to express genes that make them pluripotent through reprogramming techniques. With their unlimited proliferative capacity and multifaceted differentiation potential and circumventing the ethical problems encountered in the application of embryonic stem cells (ESC), iPSCs have a broad application in the fields of cell therapy, drug screening, and disease models and may open up new possibilities for regenerative medicine to treat diseases in the future. In this review, we begin with different reprogramming cell technologies to obtain iPSCs, including biotechnological, chemical, and physical modulation techniques, and present their respective strengths, and limitations, as well as the recent progress of research. Secondly, we review recent research advances in iPSC reprogramming-based regenerative therapies. iPSCs are now widely used to study various clinical diseases of hair follicle defects, myocardial infarction, neurological disorders, liver diseases, and spinal cord injuries. This review focuses on the translational clinical research around iPSCs as well as their potential for growth in the medical field. Finally, we summarize the overall review and look at the potential future of iPSCs in the field of cell therapy as well as tissue regeneration engineering and possible problems. We believe that the advancing iPSC research will help drive long-awaited breakthroughs in cellular therapy.
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  • 文章类型: Journal Article
    OBJECTIVE: To establish a methodological system for reprogramming rat embryonic fibroblasts (REF) into chemically induced neurons (ciNCs) via small molecule compounds to provide safe and effective donor cells for treatment of neurodegenerative diseases.
    METHODS: Based on the method established by PEI Gang\'s research group to directly reprogram human fibroblasts into neurons, the induction medium and maturation medium was optimized by replacing the coating solution, mitigating oxidative stress injury, adding neurogenic protective factors, adjusting the concentration of trichothecenes, performing small-molecule removal experiments, and carrying out immunofluorescence and Western blotting on cells at different stages of induction to validate the effect of induction.
    RESULTS: When the original protocol was used for induction, the cell survival rate was (34.24±2.77)%. After replacing the coating solution gelatin with matrigel, the cell survival rate increased to (45.41±4.27)%; after adding melatonin, the cell survival rate increased to (67.95±5.61)% and (23.43±1.42)% were transformed into neural-like cells; after adding the small molecule P7C3-A20, the cell survival rate was further increased to (76.27±1.41)%, and (39.72±4.75)% of the cells were transformed into neural-like cells. When the concentration of trichothecene was increased to 30 μmol/L, the proportion of neural-like cells reached (55.79±1.90)%; after the removal of SP600125, (86.96±2.15)% of the cells survived, and the rate of neural-like cell production increased to (63.43±1.60)%. With the optimized protocol, REF could be successfully induced into ciNC through the neural precursor cell stage, in which the neural precursor cells were able to highly express the neural precursor cell markers SRY-related HMG-box gene 2 (Sox2) and paired box 6 (Pax6) as well as neuron-specific marker tubulin 1 (Tuj1), while the expression of fiber-associated protein vimentin was reduced. After two weeks of induction of neural precursor cells in a maturation medium, most cells displayed neuronal-like cell morphology. The induced ciNCs were able to highly express the mature neuronal surface markers Tuj1 and microtubule-associated protein 2 (MAP2), while the expression of vimentin was reduced.
    CONCLUSIONS: The small molecule combinations optimized in this study can reprogram REF to ciNCs under normoxic conditions.
    目的: 建立通过小分子化合物将大鼠胚胎成纤维细胞(REF)重编程为化学诱导神经元(ciNC)的方法体系,为细胞移植治疗神经退行性疾病提供安全有效的供体细胞。方法: 以裴钢研究团队建立的人成纤维细胞直接重编程为神经元的方法为基础,通过更换包被液、缓解氧化应激损伤、添加神经源性保护因子、调整毛喉素浓度和小分子去除实验对诱导培养基和成熟培养基进行优化,并通过免疫荧光法和蛋白质印迹法验证不同诱导阶段细胞的相关蛋白质。结果: 以原方案进行诱导时,细胞存活率仅(34.24±2.77)%。包被液更换为基质胶后,细胞存活率上升到(45.41±4.27)%;添加褪黑素后细胞存活率提高至(67.95±5.61)%,(23.43±1.42)%的细胞转变为神经样细胞;添加小分子P7C3-A20后细胞存活率进一步提升至(76.27±1.41)%,(39.72±4.75)%的细胞转变为神经样细胞;毛喉素浓度提升至30 μmol/L时,神经样细胞比例达到(55.79±1.90)%;去除SP600125后,(86.96±2.15)%细胞存活,神经样细胞生成率提高至(63.43±1.60)%。以优化后的方案诱导,可经过神经前体细胞将REF诱导为ciNC。其中,神经前体细胞能够高表达神经前体细胞标志物SRY-box转录因子2、配对盒6以及神经元特异性标志物Ⅲ类β-微管蛋白,而成纤维相关蛋白波形蛋白表达量减少。神经前体细胞在成熟培养基中诱导两周后,可见大部分细胞呈神经样细胞形态,诱导后的ciNC高表达Ⅲ类β-微管蛋白和微管相关蛋白2,而成纤维相关蛋白波形蛋白表达减少。结论: 优化后的小分子组合在常氧条件下能将REF重编程为ciNC。.
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  • 文章类型: Journal Article
    造血干细胞(HSC)在肺癌微环境中表现出显著的功能和代谢改变,通过增加向髓源性抑制细胞(MDSC)的分化来促进肿瘤进展和免疫逃避。我们的目的是分析肺癌中HSC从糖酵解到氧化磷酸化(OXPHOS)的代谢转变,并确定其对HSC功能的影响。使用小鼠Lewis肺癌肺癌模型,我们对长期和短期HSC进行了代谢分析,以及多能祖细胞,比较它们在正常和癌症条件下的代谢状态。我们使用2-[N-(7-Nitrobenz-2-氧杂-1,3-三唑-4-基)氨基]-2-脱氧葡萄糖(2-NBDG)测量葡萄糖摄取,并评估乳酸水平,乙酰辅酶A,和ATP。线粒体功能通过流式细胞术评估,以及葡萄糖代谢抑制剂2-DG对HSC分化和线粒体活性的影响。肺癌条件下的HSC显示葡萄糖摄取和乳酸产生增加,随着OXPHOS活性的增加,标志着新陈代谢的转变。2-DG治疗导致T-HSCs和MDSCs减少,红细胞计数增加,强调其影响HSC代谢和分化途径的潜力。这项研究为肺癌中HSC的代谢重编程提供了新的见解,强调从糖酵解到OXPHOS的关键转变及其对癌症相关代谢途径的治疗靶向的意义。
    Hematopoietic stem cells (HSCs) exhibit significant functional and metabolic alterations within the lung cancer microenvironment, contributing to tumor progression and immune evasion by increasing differentiation into myeloid-derived suppressor cells (MDSCs). Our aim is to analyze the metabolic transition of HSCs from glycolysis to oxidative phosphorylation (OXPHOS) in lung cancer and determine its effects on HSC functionality. Using a murine Lewis Lung Carcinoma lung cancer model, we conducted metabolic profiling of long-term and short-term HSCs, as well as multipotent progenitors, comparing their metabolic states in normal and cancer conditions. We measured glucose uptake using 2-[N-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl)Amino]-2-Deoxyglucose (2-NBDG) and assessed levels of lactate, acetyl-coenzyme A, and ATP. Mitochondrial functionality was evaluated through flow cytometry, alongside the impact of the glucose metabolism inhibitor 2-DG on HSC differentiation and mitochondrial activity. HSCs under lung cancer conditions showed increased glucose uptake and lactate production, with an associated rise in OXPHOS activity, marking a metabolic shift. Treatment with 2-DG led to decreased T-HSCs and MDSCs and an increased red blood cell count, highlighting its potential to influence metabolic and differentiation pathways in HSCs. This study provides novel insights into the metabolic reprogramming of HSCs in lung cancer, emphasizing the critical shift from glycolysis to OXPHOS and its implications for the therapeutic targeting of cancer-related metabolic pathways.
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  • 文章类型: Journal Article
    巨噬细胞在先天免疫反应中起着至关重要的作用,表现出上下文相关的行为。在肿瘤微环境中,巨噬细胞以肿瘤相关或M2样巨噬细胞的形式存在,提出了重新编程的挑战。在这项研究中,我们开发了一种肽水凝胶,能够通过激活NF-κB信号通路将M0巨噬细胞极化为促炎M1巨噬细胞。重要的是,还发现该系统能够通过激活CD206受体将M2巨噬细胞重编程为促炎性M1样巨噬细胞。纳米纤维水凝胶自组装由包含先天防御调节肽和自组装促进基序的短肽,呈现密集排列的调节因子,这些调节因子与巨噬细胞膜受体多价结合,不仅使M0巨噬细胞极化,而且使M2巨噬细胞重新极化为M1样巨噬细胞。总的来说,这项工作为重新编程巨噬细胞提供了一个有前途的策略,通过重塑免疫抗性微环境来增强免疫治疗的潜力。
    Macrophages play crucial roles in the innate immune response, exhibiting context-dependent behaviors. Within the tumor microenvironment, macrophages exist as tumor-associated or M2-like macrophages, presenting reprogramming challenges. In this study, we develop a peptide hydrogel that is able to polarize M0 macrophages into pro-inflammatory M1 macrophages through the activation of NF-κB signaling pathways. Importantly, this system is also found to be capable of reprogramming M2 macrophages into pro-inflammatory M1-like macrophages by activating CD206 receptors. The nanofibrous hydrogel self-assembles from a short peptide that contains an innate defense regulator peptide and a self-assembly promoting motif, presenting densely arrayed regulators that multivalently engage with macrophage membrane receptors to not only polarize M0 macrophages but also repolarize M2 macrophages into M1-like macrophages. Overall, this work offers a promising strategy for reprogramming macrophages, holding the potential to enhance immunotherapy by remodeling immune-resistant microenvironments.
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  • 文章类型: Journal Article
    背景:尽管癌症免疫治疗取得了相当大的进展,它不适用于许多患者。对免疫检查点阻断剂的抗性来自癌症与其微环境之间的复杂相互作用。肿瘤中的代谢重编程和肿瘤微环境(TME)中的免疫细胞通过重塑免疫微环境来影响抗肿瘤免疫反应。代谢重编程已成为肿瘤发生的重要标志。然而,很少有研究关注TME和代谢重编程。因此,我们旨在使用文献计量学方法探讨TME相关代谢重编程20年来的研究现状和热门主题。
    方法:使用WebofScienceCoreCollection数据库检索关注代谢重编程和TME的研究。使用Bibliometrix对文章和评论进行了文献计量和视觉分析,VOSviewer,和城市空间。
    结果:总计,选择了在2003年至2022年之间发表的4726篇文章。出版物和引文的数量逐年增加。合作网络分析表明,美国在代谢重编程和TME研究中处于领先地位,出版物和引用量最高,从而发挥最大的影响力。在这些机构中,复旦大学表现出最高的生产力水平。免疫学前沿在该领域表现出最高的生产力。何炳志的文章贡献最多,皮尔斯·爱德华·J是被引用最多的作者。在对作者关键词进行聚类分析后,获得了四个聚类:TME,代谢重编程,免疫代谢,和豁免权。免疫代谢,糖酵解,免疫细胞,和肿瘤相关巨噬细胞是相对较新的关键词,引起了越来越多的关注。
    结论:评估了代谢重编程和TME的全面进展,这为学者们进一步推进这一充满希望的领域提供了重要信息。进一步的研究应使用跨学科方法探索与TME中免疫代谢相关的新主题。
    BACKGROUND: Despite considerable progress in cancer immunotherapy, it is not available for many patients. Resistance to immune checkpoint blockers arises from the intricate interactions between cancer and its microenvironment. Metabolic reprogramming in tumor and immune cells in the tumor microenvironment (TME) influences anti-tumor immune responses by remodeling the immune microenvironment. Metabolic reprogramming has emerged as an important hallmark of tumorigenesis. However, few studies have focused on the TME and metabolic reprogramming. Therefore, we aimed to explore the current research status and popular topics in TME-related metabolic reprogramming over a 20 years using a bibliometric approach.
    METHODS: Studies focusing on metabolic reprogramming and TME were searched using the Web of Science Core Collection database. Bibliometric and visual analyses of the articles and reviews were performed using Bibliometrix, VOSviewer, and CiteSpace.
    RESULTS: In total, 4726 articles published between 2003 and 2022 were selected. The number of publications and citations has increased annually. Cooperation network analysis indicated that the United States holds the foremost position in metabolic reprogramming and TME research with the highest volume of publications and citations, thus exerting the greatest influence. Among these institutions, Fudan University displayed the highest level of productivity. Frontiers in Immunology showed the highest degree of productivity in this field. Ho Ping-Chih made the most article contributions, and Pearce Edward J. was the most co-cited author. Four clusters were obtained after a cluster analysis of the authors\' keywords: TME, metabolic reprogramming, immunometabolism, and immunity. Immunometabolism, glycolysis, immune cells, and tumor-associated macrophages are relatively recent keywords that have attracted increasing attention.
    CONCLUSIONS: A comprehensive landscape of advancements in metabolic reprogramming and the TME was evaluated, which provided crucial information for scholars to further advance this promising field. Further research should explore new topics related to immunometabolism in the TME using a transdisciplinary approach.
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  • 文章类型: Journal Article
    单细胞测序技术的最新进展彻底改变了我们获取整个转录组数据的能力。然而,直接从这些数据中揭示潜在的转录驱动因素和细胞功能的非平衡驱动力仍然具有挑战性。我们通过从离散的单细胞RNA速度学习细胞状态矢量场,以将单细胞全局非平衡驱动力量化为景观和通量来解决这一问题。从单细胞数据中,我们量化了沃丁顿的景观,显示分化和重新编程的最佳路径偏离了天真预期的景观梯度路径,并且可能无法在有限的波动下通过景观鞍座,由于通量的存在,对细胞命运决定的动力学速率的常规过渡状态估计提出了挑战。从我们的研究中得出的一个关键见解是,干/祖细胞需要更大的能量耗散才能实现快速的细胞周期和自我更新。保持多能性。我们预测了最佳的发育途径,并阐明了细胞命运决定的成核机制,以过渡态为成核位点,先驱基因为成核种子。循环通量的概念量化了每个循环通量对细胞状态转变的贡献,促进对细胞动力学和热力学成本的理解,并提供优化生物功能的见解。我们还推断细胞-细胞相互作用和细胞类型特异性基因调控网络,包括反馈机制和相互作用强度,从单细胞组学数据预测遗传扰动对细胞命运决定的影响。本质上,我们的方法论验证了景观和通量理论,连同其相关的量化,提供了一个框架,通过高通量单细胞测序实验探索细胞分化和重编程的物理原理以及更广泛的生物过程。
    Recent advances in single-cell sequencing technology have revolutionized our ability to acquire whole transcriptome data. However, uncovering the underlying transcriptional drivers and nonequilibrium driving forces of cell function directly from these data remains challenging. We address this by learning cell state vector fields from discrete single-cell RNA velocity to quantify the single-cell global nonequilibrium driving forces as landscape and flux. From single-cell data, we quantified the Waddington landscape, showing that optimal paths for differentiation and reprogramming deviate from the naively expected landscape gradient paths and may not pass through landscape saddles at finite fluctuations, challenging conventional transition state estimation of kinetic rate for cell fate decisions due to the presence of the flux. A key insight from our study is that stem/progenitor cells necessitate greater energy dissipation for rapid cell cycles and self-renewal, maintaining pluripotency. We predict optimal developmental pathways and elucidate the nucleation mechanism of cell fate decisions, with transition states as nucleation sites and pioneer genes as nucleation seeds. The concept of loop flux quantifies the contributions of each cycle flux to cell state transitions, facilitating the understanding of cell dynamics and thermodynamic cost, and providing insights into optimizing biological functions. We also infer cell-cell interactions and cell-type-specific gene regulatory networks, encompassing feedback mechanisms and interaction intensities, predicting genetic perturbation effects on cell fate decisions from single-cell omics data. Essentially, our methodology validates the landscape and flux theory, along with its associated quantifications, offering a framework for exploring the physical principles underlying cellular differentiation and reprogramming and broader biological processes through high-throughput single-cell sequencing experiments.
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